There aren't really two separate electorates. However, the election of a President may be accomplished by ignoring much of the one that there is and concentrating efforts on heavily populated urban areas. This will be exacerbated by the National Popular Vote Interstate Compact, wherein a candidate that wins, say, Delaware, will find his state's electoral votes given to the winner of the popular vote in states in which he or she does not reside. It is an idea particularly popular with Democrats.
This was not a "mistake" on the part of the Founders, they knew they wouldn't have a country if New York's popular vote made law in Georgia and to hell with the Georgians. The Georgians had to agree to ratify the Constitution, and so their rights and sovereignty had to be respected.
When that becomes no longer the case, the very same issue will crop up just as it did in 1787. Only an idiot intent on totalitarian rule would fail to recognize this.
With the Republicans now in charge of so many state legislatures, I would expect a lot of states that had voted to enter that compact to vote to leave it.